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BIOEE 1780: Prelim 1
evolution
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a process by which populations of organisms change over time
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science
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the use of evidence to construct testable explanations and predictions of natural phenomena as well as the organization of knowledge generated through the process
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viruses
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smallest living things
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lineage
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a chain of ancestors and their descendants
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natural selection
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a mechanism that can lead to evolution; differential survival or reproduction of individuals causes some genetic types to replace (outcompete) others
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convergent evolution
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the independent origin of similar traits in separate lineages
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homologous
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characteristics are similar in two or more species because they are inherited from a common ancestor
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synapomorphy
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a derived form of a trait that is shared by a group of related species; evolved in immediate common ancestor of the group and was inherited by all the descendants;
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phylogeny
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a visual representation of the evolutionary history of populations, genes, or species
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mutations
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any change in sequence of an organism
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viral reassortment
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when genetic material from different strains gets mixed into new combinations within a single individual
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phenotypes
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measurable aspects of organisms such as morphology, physiology and behavior
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Carl Linnaeus
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father of modern taxonomy; organized all living things into a single hierarchy of groups called TAXA
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taxa
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group of organisms that a taxonomist judges to be a taxonomic unit
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taxonomy
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introduced by Carl Linnaeus; the science of describing, naming, and classifying species of living or fossil organisms
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Nicolaus Steno
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naturalist; realized remains of animals and plants were sometimes preserved and transformed into stone; argued that over time, a sea must have covered the mountains and when shelled animals died and fell to the ocean floor, they were covered in sediments and turned to rock; father of geography and stratigraphy (study of layering in rock)
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Georges Buffon
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proposed that the Earth was very old and that life had gradually changed during its history
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paleontology
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study of prehistoric life
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Georges Cuvier
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helped establish that many fossils were the remains of extinct species
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extinction
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permanent loss of a population or species, arising with the death or failure to breed of the last individual
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James Hutton
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realized rocks formed through imperceptibly slow changes; ordering of layers of rock formed and studying of fossils
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William Smith
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discovered that layers of rocks contain distinctive groups of fossils; helped to organize strata into geological history based on the location of the fossil
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Jean-Babtiste Lamarck
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developed early theory of evolution; argued that complex species had evolved from simple ones by a mechanism of heredity through which the acquired traits were passed down; species were not fixed
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epigenetic changes
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acquired through life and passed on
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Charles Darwin
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naturalist; spent five years aboard HMS Beagle gathering fossils of extinct mammals ; all living things share a common ancestry; rejected mechanisms such as Lamarck's ladder of progress (proposed simpler process based on variation and selection--descent with modification)
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Charles Lyell
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proposed that all of life on Earth formed by small changes over time--uniformitarianism; popularized Hutton's idea that the Earth was shaped by gradual processes
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Alfred Russel Wallace
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came up with a mechanism for evolution similar to Darwin's idea of natural selection; sent letter to Darwin asking ideas to be presented to the Linnaean Society
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homology
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the similarity of characteristics in different species because of a common ancestor
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homologous traits
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similar because they are inherited from a common ancestor
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analogous traits
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similar because they have converged on a shared form but not derived from a common ancestor
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Thomas Malthus
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english clergyman whom Wallace and Darwin both derived ideas from; proposed that those who could adapt to society's needs to produce useful work would be able to survive and reproduce
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adaptations
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inherited aspects of an individual that allow it to outcompete other members of a population that lack the trait; evolve through natural selection
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sexual selection
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when individuals of one sex compete with each other over access to individuals of the other sex which can lead to evolution of traits that improve an individuals chances of mating
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genetic drift
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also a mechanism of evolution; random change in the frequency of traits or genetic variants that arises across generations due to random events; most pronounced in small populations
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tips
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terminal ends of an evolutionary tree, representing species, molecules, or populations being compared
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branches
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lineages evolving through time between successive speciation events
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node
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a point in a phylogeny where a lineage splits (a speciation event)
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internal nodes
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nodes within a phylogeny representing ancestral populations or species
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clade
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an organism and all of its descendants
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monophyletic
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a term used to describe a group of organisms that form a clade
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characters
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heritable aspects of organisms that can be compared across taxa
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Taxon (or taxa)
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a group of organisms that a taxonomist judges to be a taxonomic unit, such as species or order
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cladogram
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a phylogeny constructed by grouping taxa into nested hierarchies using information from synapomorphies
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cladistics
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phylogenetic methods that construct trees by grouping taxa into nested hierarchies (clades) according to their shared derived characters (synapomorphies)
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homoplasy
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character state similarity NOT due to shared descent (e.g., produced by convergent evolution or evolutionary reversal); can create the mistaken impression that species are closely related when they are not
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convergent evolution
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the independent origin of similar traits in separate evolutionary lineages
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evolutionary reversal
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the reversion of a derived character state to its ancestral state
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systematics
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identifying synapomorphies to generate phylogenies
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exaptations
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a trait that originates performing one function and which is later co-opted for a new function (ex. feathers-evolved originally for other functions than flight i.e. insulation, courtship display, and nest brooding)
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Australopithecines
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members of the hominid genus Australopithecus; still had snouts and chimpanzee-sized brains but had more adaptations for walking upright and arboreal life; evidence that bipedalism evolved long before an increase in brain size
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mammalian ear
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made up of modified parts of the lower jaw
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coalescence
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the process by which, looking back through time, the genealogy of any pair of homologous alleles merges in a common ancestor
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genealogies
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possible to trace back through time, reconstructing when mutations generated new alleles and how these alleles subsequently spread
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gene tree
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the branched genealogical lineage of homologous alleles that traces their evolution back to an ancestral allele
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maximum parsimony
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a statistical method for reconstructing phylogenies which identifies the tree topology that minimizes the total amount of change, or the number of steps, required to fit the data to the tree
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positive selection
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accumulation of an unusually high level of substitutions that change the structure of proteins
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purifying selection
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also called negative selection; removes deleterious alleles form a population; common form of stabilizing selection
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bootstrapping
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a statistical method for estimating the strength of evidence that a particular node in a phylogeny exists
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distance-matrix methods
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methods that construct phylogenetic trees by clustering taxa based on the proximity (or distance) between their DNA or protein sequences; place closely related sequences under the same interior node, and they estimate branch lengths from the observed distances between sequences
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neighbor-joining
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a distance method for reconstructing phylogenies; identifies the tree topology with the shortest possible branch lengths given the data
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Maximum likelihood methods
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focus on finding the tree that is "most likely" given the data set and model; begin with an explicit model of evolution at the molecular level and used to evaluate how well data support a given tree; compare likelihood scores for many different possible trees, and find tree that best fits data and model for molecular evolution
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Bayesian methods
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focus on evaluating the probability of a given tree being correct; start with possible tree and then make small changes to its topology over and over again and then converge on a set of most likely trees
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Restriction enzymes
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enzymes produced mostly by bacteria that recognize specific nucleotide sequences within DNA; cleave the DNA, resulting in fragments of different lengths depending on the source of the enzyme
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micro satellites
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noncoding stretches of DNA containing strings of short, repeated segments; the number of repetitive segments can be highly polymorphic so these are valuable genetic characters for comparing populations and assigning relatedness among individuals
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synonymous substitutions
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mutations that do not alter the amino acid sequence of a protein; these mutations do not affect the protein an organism produces, so they are less prone to selection and often free from selection completely
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non-synonomous substitutions
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also called replacement substitutions; mutations that alter the amino acid sequence of a protein; these can affect the phenotype and are therefore more subject to selection
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molecular clock
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a method used to determine time based on base-pair substitutions; use the rates of molecular change to deduce the divergence time between two lineages in a phylogeny; work best when they can be calibrated with other markers of time, such as fossils with known ages
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neutral theory of molecular evolution
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describes the pattern of nucleotide sequence evolution under the forces of mutation and random genetic drift in the absence of selection; under these conditions, substitution rate should equal the mutation rate
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domains
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Archaea, Bacteria, and Eukarya
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prokaryotes
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domain with a lack of a nucleus and of membrane-closed organelles
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peptidoglycan
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contained in the cell walls of almost all bacteria; lacking in the cell walls of archaea and eukarya
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Gram stain
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laboratory technique used to classify most types of bacteria into two distinct groups, Gram-positive and Gram-negative; smear of bacterial cells on a microscope slide is soaked in a violet dye and treated with iodine then washed with alcohol and counterstained with red safranin
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gram-positive bacteria
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retain the purple dye; have a thick cell wall containing about five times as much peptidoglycan
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gram-negative bacteria
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retain the red safranin counter stain; have a periplasmic space between the cell membrane and the distinct outer membrane
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spirilla
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bacteria in the shape of spirals
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bacilli
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bacteria in the shape of rods
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cocci
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bacteria in the shape of a sphere
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lateral gene transfer
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the transfer of genes from one species to another, common among bacteria and archaea
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high-GC gram positives
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produce important antibiotics; also known as actinobacteria; have more G-C nucleotide base pairs; develop an elaborately branched system of filaments that resembles the filamentous growth habit of fungi
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low-GC gram positives
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also known as firmicutes; low ratio of G-C nucleotide base pairs; can produce heat-resistant structures called endospores
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mycoplasmas
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group of low-GC Gram-positives that lack cell walls and are among the smallest cellular organisms
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cyanobacteria
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blue-green bacteria; photosynthetic bacteria that utilize Co2 and water and release oxygen into the atmosphere; may be unicellular or multicellular; use chlorophyll a for photosynthesis and fix nitrogen; extensive internal membranes
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spirochetes
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have unique structures called axial filaments that allow them to move in a corkscrew-like manner (ex. syphilis, lyme disease)
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proteobacteria
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mitochondria of eukaryotes derived through endosymbiosis of this; largest number of known species of bacteria; very diverse: aerobes, anaerobes, heterotrophs, photoautotrophs, chemoautotrophs, nitrogen fixers, big, small
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autotroph
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fix their own carbon
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heterotroph
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ingest already fixed carbon
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photoautotrophs
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an organism that obtains energy from light and carbon from carbon dioxide
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chemoheterotroph
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an organism that must obtain both carbon and energy from organic substances; critically important as decomposers (degrading organic matter)
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Rhizobia
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live in root nodules; leguminous plants that create these clumps that are colonized by bacteria and fix nitrogen and put it into the soil as a usable form for the plant
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Binary Fission
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asexual reproduction all prokaryotes do; replicated chromosomes then split cell wall and divide continuously
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Conjugation
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genetic exchange between two individuals, separate from the process of reproduction (which occurs by binary fission)
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Phage conversion (transduction)
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genetic exchange mediated by a phage (virus); phage attacks bacterium and inserts DNA/RNA which then gets incorporated into the host genome
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Transformation
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damaged cell leaks DNA other cells transport it through the membrane and incorporate it into their DNA
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chlamydias
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very small, all are obligate parasites; most common STD in US
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extremophiles
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archaea able to live under extreme conditions
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acidophile
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able to live in extremely acidic environments
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halophile
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able to live in hypertonic and alkali environment (very basic)
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methanogens
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contribute to global warming; anaerobic; found in hydrothermal vents, paddy fields, and mammalian guts
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mitochondria
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derived from a proteobacterium; powerhouse of the cell; produces ATP
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endosymbiosis
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incomplete phagocytosis of prokaryotes results in membrane bound organelles of eukaryotes; acquisition of a complete organism
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chloroplasts
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derived from a cyanobacterium (primary endosymbiotic event); represents a synapomorphy of the Plantae; found in unicellular algae
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bacterial mating
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conjugation and other processes that lead to genetic exchange within a bacterial species (different from LGT which is between species)
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protists
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eukarya that are not animals, fungi or plants
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alveolates
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sacs (alveoli) under plasma membrane; ciliates and dinoflagellates
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ciliates
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a group of alveolates which are covered with small hairlike strictures called cilia; aquatic: freshwater, marine, soil, endosymbionts; can be very complex, multinuclear
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dinoflagellates
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two flagella: one in an equatorial grove, the other running along the external plates of cellular (the chin); a few are freshwater, many abundant as marine plankton; endosymbionts of corals; can lead to neurotoxic red tides or bioluminescence
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coral bleaching
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corals lose the dinoflagellate symbionts when the water heats up with UV radiation and die
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plasmodium
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obligate intracellular parasites; specialized structure for getting into RBC's-complex of proteins for penetration of host cells; still have plastid but it doesn't have chloroplast function; leads to malaria
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Stramenophiles
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synapomorphy: 2 unequal flagella, one of which has tubular hairs; many have lost flagella--2 major groups: brown algae and diatoms
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brown algae
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color from carotenoid; almost all are marine photoautotrophs; largest protists
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diatoms
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silica "petri dishes"; photoautotrophs; almost all are marine; major component of plankton because of photosynthetic function; fix 20% of all carbon on the planet
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excavates
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2000 species; mitochondria absent or reduced (mitoses) in some groups of excavates; associated with anaerobic conditions (no oxygen, no need for mitochondria to function); guard, euglena, trypanosome
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giardia
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loss of mitochondrial function; multiple flagella; most common intestinal parasite in US, water-borne, STD
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euglena
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can be photoautotrophs and chemoheterotrophs if they are denied correct conditions; primarily freshwater
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amoebozoans
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Inhabit aquatic and terrestial environments; have many forms, some living as multicellular colonies; Are heterotrophic and move using pseudopodia.
They ingest other protists and prokaryotes through the cell membranes by phagocytosis
they look like lightbulbs
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slime molds
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multicellular amoebozoans
two types: Plasmodial (multinucleate mush of cytoplasm oozing around for movement of the plasmodium)
cellular (the individuals are the ones that move around--can develop fruiting structures with resistant asexual spores)
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psuedopods
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Means "false feet." This is how amoeba and white blood cells move from place to place.
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flagella
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A long, whip-like filament that helps in cell motility. Many bacteria are flagellated, and sperm are flagellated.
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plantae
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Kingdom of multicellular photosynthetic autotrophs that have cell walls containing cellulose
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Glaucophytes
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plantae; unicellular; freshwater organisms; likely the first group to diverge; chloroplasts retain a bit of peptidoglycan between inner and outer membrane, which is normally only in prokaryotes such as cyanobacteria (this feature has been lost in other plantae groups)
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chlorophytes
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The most abundant and diverse group of green algae, including freshwater, marine, and terrestrial forms; some are unicellular, others colonial, and still others multicellular.
use chlorophylls a and b in their photosynthesis.
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red algae
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Reddish accessory pigment phycoerythrin masks green chloroplasts in low light
~4,000 species, marine, multicellular, often attach by holdfast
Secrete calcium carbonate, enhance formation of coral reefs
Lack peptidoglycan
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embryophytes
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Land plants; internally protected embryo
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liverworts
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Gametophytes are green, leaf like layers that lie flat on the ground. attach by hair-like rhizoids
Gametophyte is dominant generation
9000 species
evolved metabolic pathway for athocyanidin pigments
first with protected embryo
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mosses
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gametophyte is the dominant generation
Larger, more complex than liverworts
15,000 species
Moist terrestrial habitats, form lush mats
Decaying layers in water form peat bogs
first with stomata
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stomata
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A microscopic pore surrounded by guard cells in the epidermis of leaves and stems that allows gas exchange between the environment and the interior of the plant while controlling water loss.
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chlorophyll a
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A photosynthetic pigment that participates directly in the light reactions, which convert solar energy to chemical energy.
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chlorophyll b
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A type of yellow-green accessory photosynthetic pigment that transfers energy to chlorophyll a.
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anthocyanidin
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Pigment absorbs UV (240, 280, 330nm) and blue (495nm)
Protects the plant from UV damage
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alternation of generations
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the alternation between the haploid gametophyte and the diploid sporophyte in a plant's life cycle
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haploid
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1 set of chromosomes
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diploid
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2 sets of chromosomes
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sporophyte
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Diploid, or spore-producing, phase of an organism
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gametophyte
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Haploid, or gamete-producing, phase of an organism
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sporangia
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A capsule in fungi and plants in which meiosis occurs and haploid spores develop.
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lycophytes
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club mosses
Common in moist woodland understory
~1,200 species
Comprised vast forests in Carboniferous Period
-true branching roots
-had microphylls-small vascularized leaves
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horsetails
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-seedless vascular plant with jointed stems; needlelike branches
-15 species
-gametophyte is small, sporophyte is big
-secondary reduction of leaves
-flagellated gametes
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gymnosperms
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"Naked seeds", such as pine cones and other conifers.
-sporophyte dominant
-mode of dispersal is by seeds.
-multicellular gametophyte, but no longer photosynthetic
1100
cycads, gingkos, conifers
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angiosperms
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"covered seed"
250,00 species
synapomorphies: fruit & flowers
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ferns
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12000 species
gametophyte is reduced but photosynthetic
sporophyte is big
gametes have flagella and need water
megaphylls a major innovation of ancestors
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microphylls
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smaller leaves
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megaphylls
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large leaves
have branching vascular system
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seeds
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Consists of an embryonic sporophyte plant, supply food for embryo, and is a protective outer coat.
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xylem
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cells die and become hollow for:
-transport of water and minerals
-structural support
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phloem
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vascular tissue
brings the products of photosynthesis from sites of production to the sites where they are used or stored
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tracheids
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A water-conducting and supportive element of xylem composed of long, thin cells with tapered ends and walls hardened with lignin.
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pollen
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male gametophyte
each grain has multiple vegetative non-reproductive cells
has one reproductive cell that divides to make sperm & pollen tube
An adaptation that eliminated the need for sperm to swim through water to fertilize an egg.
Has a protective coat to prevent them from drying out.
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roots
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Absorb nutrients from soil, anchor the plant, and store food
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fruits
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-swollen ovarian tissue surrounding the seed(s)
-some evolved for seed dispersal
-some provide fertilizer for the seed
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flowers
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-wind pollinated
-co-evolved with animal pollinators
-showy to advertise nectar reward
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Opisthokonts
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organisms from an ancestor with posterior flagellum (includes fungi, animals, and some protists)
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fungi
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A kingdom made up of nongreen, eukaryotic organisms
-chitin in cell walls
-reproduce by using spores
-get food by breaking down substances in their surroundings and absorbing the nutrients (absorptive heterotrophy)
-100,000 species
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microsporida
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-unicellular, tiniest eukaryotes
-highly reduced fungi (no mitochondria)
-intracellular parasites of animals
-polar tube on them injects contents of spore into host
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arbuscular mycorrhizal fungi
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-represent a plant-fungi partnership in which they penetrate the cell wall and form tree structures but in not plasma membrane
-plant gets nutrients from the fungus and the fungus gets the product of photosynthesis
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chytrids
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-paraphyletic group
-aquatic, single or multicellular
-Fungi that include the parasite linked to large-scale frog extinction
-parasitic
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lichens
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Composite organisms consisting of a symbiotic association of a fungus with a photosynthetic partner(green algae)
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dikarya
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sac fungi and club fungi
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Basidiomycota
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-club fungi
=-"true fungi"
-edible and poisonous
-synapomorphy: the basidium (cell in which meiosis occurs)
-30,000 species
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Ascomycota
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-sac fungi
-mutualistic fungi type
-64,000 species
-morels, most yeasts, molds, and lichens
-synapomorphy: the ascus
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absorptive heterotroph
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An organism (usually a fungus) that obtains its food by secreting digestive enzymes into the environment to break down large food molecules, then absorbing the breakdown products.
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saprobe
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fungi that take up nutrients from nonliving organic matter
ezymes digest cellulose, lignin, keratin
"earth's garbage disposal"
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parasite
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fungi that take up nutrients from parasitic interactions, with varying dependence on their host
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mutualism
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when two species are close in association and both parties benefit
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chitin
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Complex carbohydrate that makes up the cell walls of fungi
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hyphae
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Long filament of cells that makes up the body of fungus.
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mycelium
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A mat of hyphae that forms the body of a fungus; , The part of the fungus responsible for absorption of nutrients.
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fruiting structure
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A sporebearing structure on fungi body
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mycorrhizae
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A mutualistic association of plant roots and fungus
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mating types
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discrete kinds of a mushroom's haploid mycelia that contain distinct nuclei, and only certain types are sexually compatible
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dikaryotic
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Referring to a fungal mycelium with two haploid nuclei per cell, one from each parent.
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arbuscule
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-branched, tree-shaped structures that the hyphae inside the root cells form
-site of nutrient exchange in the AM fungi
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mycology
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Study of fungi
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